My polaris is not working and I have LOTS of leaves in the bottom of my pool. To manually vacuum, do I do this to "waste"? I am wondering if I vacuum on "filter" whether the leaves will clog up my pool pump.

For the leaves, it won't matter whether you vacuum on filter or waste, as the leaves will all collect in the pump strainer basket.

If you have a lot of leaves, I would recommend vacuuming slowly. I find that if I try to vacuum up too many leave too quickly, that I end of clogging the vacuum hose, and that can be a real pain to unclog.